rutilstimflutre: Timothee Flutre's personal R code

writeSegregJoinMap

R Documentation

Write genotypes for JoinMap/MapQTL

Description

Write genotype data in the JoinMap format into a "loc" file used by this software.

Usage

writeSegregJoinMap(
  pop.name,
  pop.type = "CP",
  locus,
  segregs,
  genos,
  phases = NULL,
  classifs = NULL,
  file,
  save.ind.names = TRUE,
  na.string = "--",
  verbose = 1
)

Arguments

`pop.name`	name of the population
`pop.type`	type of the population
`locus`	vector of locus names; should be shorter or equal to 20 characters, otherwise a warning will be issued; should be in the same order as the rows of the "genos" argument
`segregs`	vector of segregation types; should be in the same order as the rows of the "genos" argument
`genos`	data frame containing genotypes encoded in the JoinMap format, similar to the output from `genoClasses2JoinMap`
`phases`	vector of phase types (optional; should be in the same order as the rows of the "genos" argument)
`classifs`	vector of classification types (optional; should be in the same order as the rows of the "genos" argument)
`file`	name of the file in which the data will be saved (will be compressed if ends with ".gz" and "gzip" is available in the PATH)
`save.ind.names`	if TRUE, individual names will be saved at the end of the file
`na.string`	character to replace NA's in "genos"
`verbose`	verbosity level (0/1)

Value

nothing

Author(s)

Timothee Flutre

Examples

## Not run: ## make fake data
nb.snps <- 6
x <- data.frame(par1=c("AA", "GC", "CG", "AT", NA, "AA"),
                par2=c("AT", "GC", "GG", "AT", "AT", "AT"),
                off1=c("AA", "GG", "CG", "AA", "AA", "AT"),
                off2=c("AT", "GG", "CG", "AT", "AT", "AA"),
                off3=c("AT", "GG", "GG", "TT", "TT", NA),
                off4=c(NA, NA, NA, NA, NA, NA),
                row.names=paste0("snp", 1:nb.snps),
                stringsAsFactors=FALSE)
jm <- genoClasses2JoinMap(x=x, reformat.input=TRUE, thresh.na=2, verbose=1)
idx <- which(! is.na(jm$seg))
writeSegregJoinMap(pop.name="test", pop.type="CP", locus=rownames(jm[idx,]),
                   segregs=jm[idx,"seg"], genos=jm[idx,-c(1:9)], file="test.txt")

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.